52,836 research outputs found

    Validation analysis of genes potentially involved in the squamous differentiation response of oral carcinoma cells to cell cycle stress

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    Head and neck cancer is rated as the sixth most common cancer worldwide among which oral squamous cell carcinoma (OSCC) is the most frequently diagnosed type. Human Papilloma Virus infection and the intake of tobacco and alcohol are the main risk factors in this pathology. The accumulation of genetic mutations and damage are thought to induce the development of cancer. Head and Neck epithelia possess different DNA-damage response mechanisms. The host laboratory has previously described a novel epidermal keratinocyte DNA-damage differentiation response (DDDR) to cell cycle stress. They also have found this squamous DDDR in non-lesional keratinocytes from head and neck. The loss of this mechanism would allow cells with genomic instability to proliferate resulting in carcinogenesis. Currently, the molecules controlling the DDDR are unknown. The lab recently run RNAseq experiments on oral carcinoma cells that respond or do not respond to the DDDR. I have studied five of the genes selected in the RNAseq study as potential regulators of the DDDR. We induced DDDR with Nocodazole (mitotic inhibitor), a drug used as a chemotherapy agent in four OSCCs. We observed that OSCC samples present an altered DDDR pattern. We therefore studied upon Nocodazole treatment, by RTqPCR, immunofluorescence or western blot, the expression of the candidate genes as well as two squamous differentiation markers (IVL and KRT13). The results show changes of four of the genes that suggest they might participate in the DDDR response. These genes have functions in cell cycle-dependent protein degradation, in cell differentiation, in suppression of proliferation, in DNA endoreplication or in programmed cell death. Although these assertions have to be validated with future experiments, the findings open a new path for an involvement of four of the genes analysed, in the squamous DDDR.Máster en Biología Molecular y Biomedicin

    Community engagement in Cutaneous Leishmaniasis research in Brazil, Ethiopia, and Sri Lanka: A decolonial approach for global health.

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    Cutaneous leishmaniasis (CL) is a parasitic skin disease endemic in at least 88 countries where it presents an urgent, albeit often "neglected" public health problem. In this paper, we discuss our model of decolonial community engagement in the ECLIPSE global health research program, which aims to improve physical and mental health outcomes for people with CL. The ECLIPSE program has four interlinked phases and underpinning each of these phases is sustained and robust community engagement and involvement that guides and informs all activities in ECLIPSE. Our decolonial approach implies that the model for community engagement will be different in Brazil, Ethiopia and Sri Lanka. Indeed, we adopt a critical anthropological approach to engaging with community members and it is precisely this approach we evaluate in this paper. The data and material we draw on were collected through qualitative research methods during community engagement activities. We established 13 Community Advisory Groups (CAGs): in Brazil ( = 4), Ethiopia ( = 6), and Sri Lanka ( = 3). We identified four overarching themes during a thematic analysis of the data set: (1) Establishing community advisory groups, (2) CAG membership and community representation, (3) Culturally appropriate and context-bespoke engagement, and (4) Relationships between researchers and community members. During our first period of ECLIPSE community engagement, we have debunked myths (for instance about communities being "disempowered"), critiqued our own practices (changing approaches in bringing together CAG members) and celebrated successes (notably fruitful online engagement during a challenging COVID-19 pandemic context). Our evaluation revealed a gap between the exemplary community engagement frameworks available in the literature and the messy, everyday reality of working in communities. In the ECLIPSE program, we have translated ideal(istic) principles espoused by such community engagement guidance into the practical realities of "doing engagement" in low-resourced communities. Our community engagement was underpinned by such ideal principles, but adapted to local sociocultural contexts, working within certain funding and regulatory constraints imposed on researchers. We conclude with a set of lessons learned and recommendations for the conduct of decolonial community engagement in global health research. [Abstract copyright: Copyright © 2022 Polidano, Parton, Agampodi, Agampodi, Haileselassie, Lalani, Mota, Price, Rodrigues, Tafere, Trad, Zerihun and Dikomitis.

    The Genetics of Pain: An exploration of gene-by-environment interactions and their effects on pain

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    The findings presented in this dissertation are part of the bigger SYMBIOME project which aims to use the biopsychosocial model of pain to develop a prognostic clinical phenotype for people that experience musculoskeletal (MSK) trauma. Chapter 2 presents an exploratory analysis to assess the relationships between genetic polymorphisms and pain severity and interference. Early childhood trauma was also explored as a moderator between genetic polymorphisms and pain outcomes. For pain severity, major allele carriers (A/A and G/A) of FKBP5 rs9394314 reported significantly higher scores than minor allele carriers (G/G). Further, major allele carriers who had at least one adverse childhood experience (ACE) reported significantly higher scores than minor allele carriers with at least one ACE. For pain interference, minor allele carriers (G/G) of CNR2 rs2501431 scored significantly higher than major allele carriers (A/A and G/A). Chapter 3 presents a cluster analysis that combines genotypes of FKBP5 rs9394314 and CNR2 rs2501431 to explore meaningful relationships with pain and trauma-related distress. ACE was also explored as a moderator of these relationships. Three clusters were identified where the second cluster characterized by major allele carriers of rs9394314 and minor allele carriers of rs2501431 reported significantly higher pain-related functional interference scores. Participants in the second cluster with at least one ACE reported higher pain interference and traumatic distress scores compared to the third cluster, while participants in the first cluster with at least one ACE reported higher pain severity compared to the first cluster. Chapter 4 presents genomic structural equation models (SEM) that explore the relationships of genotypes with trauma-related distress using the traumatic injuries distress scale (TIDS), ACE, and recovery outcomes. The results demonstrate a relationship between TIDS and recovery outcomes, and an indirect relationship between FKBP5 rs9394314 and recovery outcomes exist which is mediated by TIDS. Major allele carriers of FKBP5 rs9394314 reported higher TIDS scores, which was also demonstrated for participants that had at least one ACE. Major allele carriers that scored higher on the TIDS were predicted to be in the none-recovered category. These results support the notion that gene-x-environment interactions may play an important role in pain and recovery

    Study on the concordance between different SNP‚Äźgenotyping platforms in sheep

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    .Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic predictionS

    Biocontrol as a key component to manage brown rot on cherry

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    Brown rot, caused by Monilinia spp., is one of the most important diseases in stone fruits worldwide. Brown rot can cause blossom wilts and fruit rots in the orchard as well as latent infections of fruit, leading to post-harvest fruit decaying. Current control methods rely on scheduled spraying of fungicides. However, the continuing pressure to reduce fungicide use has seen an increase in research into alternative management methods, such as biological control. NIAB EMR recently identified two microbes that significantly reduced sporulation of Monilinia laxa under laboratory conditions. These two isolates were a bacterial species Bacillus subtilis (B91) and yeast-like fungus Aureobasidium pullulans (Y126) and are currently being formulated into commercial products. We are investigating how to optimise the use of these two potential biocontrol products in practice, in terms of suppressing Monilinia sporulation on overwintered mummies and preventing infection of blossoms and fruits. When applied to mummified fruits in winter Y126’s population was stable through the winter but at a low concentration. The B91 survived a little longer with the population reaching that of the control group by week 4. Neither Biological control (BCA) treatments had an affected the population of M. laxa when compared to the control treatment of sterile distilled water. The interaction time between the BCAs and M. laxa showed the longer the interaction time the lower the spore count of M. laxa. Another study was performed looking into the ability of our BCAs to colonise and survive on blossoms. B91 did not survive well on blossoms but could survive on fruits. However, its antagonistic compounds need to be in relatively high concentration to be effective against M. laxa. Therefore, it is best used as a fungicide, ensuring the antagonistic compounds are at a high concentration when applied in the field. Y126 can persist throughout the season and was marginally, though not statistically significantly, more effective at long term reduction in M. laxa. This could be because Y126 works through competition, therefore the interaction time with the pathogen could be important for efficacy and something worth investigating further. The difference between the BCAs highlights the need to understand each BCA’s ecology to ensure maximum efficacy. In a latent infection experiment, we inoculated trees with M. laxa and then treated them with the two biocontrol isolates two weeks before harvest. Post-harvest disease development was assessed after four days of storage in 2019 and two weeks in 2020. There was a significant reduction in rot incidence (p < 0.001) of 29% (Y126) and 27% (B91) in 2019 and 62 % (Y126) and 80 % (B91) in 2020 when the harvested fruit was stored at cold store levels. With new products to be introduced into the environment, it's important to understand the effects they may have on the plant's microbiome. Using next-generation sequencing techniques, we looked at the impact B91 and Y126 has on the blossom and cherry microbiomes. There was a treatment effect in both the bacterial and fungal communities on the blossom and ripe cherry. But the biggest variability was between blocks (Geographical effect) and between the years in which we experimented (p < 0.0001). This research will assist in the development of management strategies, especially spray timings for brown rot on stone fruit, integrating BCAs with other management practices

    Iam hiQ‚ÄĒa novel pair of accuracy indices for imputed genotypes

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    Background Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imputed is fundamental. Several accuracy measures have been proposed and some are implemented in imputation software, unfortunately diversely across platforms. In the present paper, we introduce Iam hiQ, an independent pair of accuracy measures that can be applied to dosage files, the output of all imputation software. Iam (imputation accuracy measure) quantifies the average amount of individual-specific versus population-specific genotype information in a linear manner. hiQ (heterogeneity in quantities of dosages) addresses the inter-individual heterogeneity between dosages of a marker across the sample at hand. Results Applying both measures to a large case‚Äďcontrol sample of the International Lung Cancer Consortium (ILCCO), comprising 27,065 individuals, we found meaningful thresholds for Iam and hiQ suitable to classify markers of poor accuracy. We demonstrate how Manhattan-like plots and moving averages of Iam and hiQ can be useful to identify regions enriched with less accurate imputed markers, whereas these regions would by missed when applying the accuracy measure info (implemented in IMPUTE2). Conclusion We recommend using Iam hiQ additional to other accuracy scores for variant filtering before stepping into the analysis of imputed GWAS data

    Incentivising research data sharing : a scoping review

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    Background: Numerous mechanisms exist to incentivise researchers to share their data. This scoping review aims to identify and summarise evidence of the efficacy of different interventions to promote open data practices and provide an overview of current research. Methods: This scoping review is based on data identified from Web of Science and LISTA, limited from 2016 to 2021. A total of 1128 papers were screened, with 38 items being included. Items were selected if they focused on designing or evaluating an intervention or presenting an initiative to incentivise sharing. Items comprised a mixture of research papers, opinion pieces and descriptive articles. Results: Seven major themes in the literature were identified: publisher/journal data sharing policies, metrics, software solutions, research data sharing agreements in general, open science ‚Äėbadges‚Äô, funder mandates, and initiatives. Conclusions: A number of key messages for data sharing include: the need to build on existing cultures and practices, meeting people where they are and tailoring interventions to support them; the importance of publicising and explaining the policy/service widely; the need to have disciplinary data champions to model good practice and drive cultural change; the requirement to resource interventions properly; and the imperative to provide robust technical infrastructure and protocols, such as labelling of data sets, use of DOIs, data standards and use of data repositories

    Epigenetics : a catalyst of plant immunity against pathogens

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    The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution
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